I agree with Peter, they could have made it so you could choose to be a member of the boarding party (or direct the boarding party), leaving the ship in the control of a serviceable AI. And if a player's ship was boarded, they could choose to leave the ship as an AI and fight against the boarding party. Or players could let the boarding parties and security forces defending the ship be AIs, and choose to remain in command of the ship. It would just be another choice, allowing players to play the way they want to play.

It seems to me that this game wants people to find their own way to play the game, offering a lot of choices, but they're unwilling to go the extra mile and let players *really* choose. I don't think it would be that much harder to implement something like this in the game. Here's hoping they're *listening* and get this system in the game ASAP; if not at launch, then soon thereafter.